An academic article which discusses exactly that, examining sources such as "the diaries of aristocrats and priests, many statues and pictures such as clay figures called "Haniwa", and Buddhist images or portraits."

HISTORICAL STUDY OF SITTING IN JAPAN: WITH "SEIZA" AS MAIN TOPIC Yusei Tazaki Mukogawa Women’s University, Japan http://www.mukogawa-u.ac.jp/~iasu2012/pdf/iaSU2012_Proceedings_205.pdf

The evidence seems to suggest that aristocrats, and samurai used to sit in "agura" or crosslegged on the ground, and common people would also do the same and squat in rainy weather.

Seiza was seen in religious scenes as a form of respect, and also used by inferiors as a position that was easy to quickly move out in order to serve their superiors. Buddhism and the tea ceremony (and more raised floor houses with tatami) spread the use of seiza more widely.